Clustering of yeast protein-protein interaction networks in the context of overlapping yeast genetic interaction data reveals possible pathway interactions between three well-known complexes. (A) The overall results of MCL clustering of the Collins et al.,  data set showing the largest clusters. Nodes are colored according to cluster. Thick edges represent intra-cluster edges and thin edges are inter-cluster. Three complexes are highlighted: SWR1, SET1, and prefoldin. (B) Closeup of the prefoldin complex from the chromosome biology EMAP (Additional File 3). Note that there is a very strong positive genetic interaction (yellow) between all of the genes in the complex except for GIM3 and GIM4, which is still positive overall. (C) Closeup of the prefoldin complex from the RNA processing EMAP (Additional File 4). The closeup shows the same slightly decreased interaction for GIM3 and GIM4. (D) The section of the chromosome biology EMAP with the prefoldin complex showing the strong negative interaction with SWR1 and positive interaction with SET1.